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  • Cybergenetics :: Computer automation of STR scoring for forensic databases
    Forensic Human Identification in the Millennium London UK 26 Oct 1999 Downloads PowerPoint presentation and handout for the International Conference on Forensic Human Identification in the Millennium 1999 talk Download Handout Download PowerPoint Download Paper Abstract Forensic databases are becoming an increasingly valuable law enforcement tool for convicting repeat offenders and exonerating the innocent However constructing such databases is quite laborious After generating STR profiles in the lab people expend even greater effort visually reviewing the data before it enters the database All artifacts must be detected and no error can be tolerated With millions of samples to analyze every year this has become a formidable task We have developed software analysis methods that can automate this data review and potentially eliminate 90 of the work Our fully automated TrueAllele 153 system inputs raw fluorescent DNA sequencer gel files processes the gel image separating colors tracking and sizing lanes and analyzes the STR experiments quantitating and sizing peaks comparing with ladder peaks calling alleles For each allele call TrueAllele assigns a quality score and applies artifact detection rules These quality checks enable a user to focus on just the 5 10 of suspect data thereby eliminating most of the review

    Original URL path: http://www.cybgen.com/information/presentations/1999/ICFHIM/Perlin_Computer_automation_of_STR_scoring_for_forensic_databases/page.shtml (2016-02-12)
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  • Cybergenetics :: Further Exploration of TrueAllele Casework
    have been performed These studies examined 1 What effect does the use of the differential degradation feature have on the log LR of contributors to a differentially degraded mixture 2 What happens to the TA analysis when either a greater or fewer number of contributors is solved for than are actually in the mixture and 3 What happens to the log LR of contributors when the DNA sample is over amplified loaded The use of the differential degradation feature produced only a small 1 log LR unit change if any for contributors in differentially degraded mixtures However it may have affected how readily the sample was separated resulting in fewer computer runs This improvement may be due to a more accurate assessment of the mixture weights when differential degradation is taken into account When a greater number of contributors was hypothesized for TA analysis than was in the mixture typically there was a small reduction if any effect on the log LR values generated When a smaller number of contributors was hypothesized than was in the mixture it often dramatically reduced the log LR of donors This is consistent with how the TA modeling works restricting the number of contributors

    Original URL path: http://www.cybgen.com/information/presentations/2015/ISHI/Greenspoon-Further-exploration-of-TrueAllele-Casework/page.shtml (2016-02-12)
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  • Cybergenetics :: TrueAllele Speed for Grand Jury Need: Same Day Reporting of Complex Mixtures
    with possession of a manufactured weapon in prison In November of that year the police sent the shiv to the Kern Regional Crime Laboratory KRCL for DNA analysis In March of 2012 a KRCL analyst advised the Deputy District Attorney that touch items do not produce good DNA results and are often inconclusive So in May the unanalyzed shiv was returned to the police In November of that year the police sent the shiv to the Kern Regional Crime Laboratory KRCL for DNA analysis In March of 2012 a KRCL analyst advised the Deputy District Attorney that touch items do not produce good DNA results and are often inconclusive So in May the unanalyzed shiv was returned to the police The private lab calculated combined probability of inclusion CPI statistics 1 of 4 Caucasians could not be excluded from the handle mixture 1 of 8 African American could not be excluded and 1 of 6 Hispanic persons The defense attorney elected to not use these relatively uninformative CPI results In 2013 the KRCL prepared to interpret DNA mixtures using its new TrueAllele 174 Casework system Their TrueAllele validation study examined up to five unknown contributors on laboratory prepared mixed samples Forensic analysts were trained and certified on how to use the probabilistic genotyping system On October 10 2013 the KRCL deployed TrueAllele in house for automated computer interpretation of forensic DNA evidence By year s end the KRCL was poised for computer analysis of complex DNA mixtures On February 7 2014 KRCL received the private lab s fsa electronic data files and entered them into TrueAllele The computer s genotype modeling excluded Ford from the screw and the string However TrueAllele found that a match between a minor contributor to the handle and Anthony Ford was 1 4 million times

    Original URL path: http://www.cybgen.com/information/presentations/2014/ISHI/Perlin-Inconclusive-three-person-mixture-yields-guilty-plea-TrueAllele-genotype-revival/page.shtml (2016-02-12)
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  • Cybergenetics :: TrueAllele Speed for Grand Jury Need: Same Day Reporting of Complex Mixtures
    Yet there is a clear societal need for more speed and information when reporting mixtures in important cases Fast parallel computing by a validated genotype probability modeling system can overcome this mixture interpretation bottleneck providing rapid turnaround time and preserving identification information Cybergenetics TrueAllele 174 Casework is regularly used to rapidly solve DNA mixtures that have three four or more unknown contributors By successively peeling away genotype layers TrueAllele can dissect complex mixtures often of related individuals Out of twenty TrueAllele validation studies seven are published peer reviewed papers At 2 pm on Wednesday December 11 2013 a New York State district attorney contacted Cybergenetics His rape case was going to a Grand Jury the next day The crime lab had done STR analysis on the inside of a glove One swab was reported as consistent with the victim major and two male donors minors but excluded the suspect Another swab contained at least three contributors but due to the complexity of the genetic information no comparisons were made New DNA results by morning could postpone the case a week At 4 30 pm the lab emailed their fsa data files to Cybergenetics By 5 pm the peak height data were analyzed and uploaded to a TrueAllele server The computer was asked twelve separate questions consider both evidence items in duplicate computer runs and assume three contributors under different scenarios all unknown victim known and victim and elimination both known At 5 30 pm twelve computer cores set to work on their assigned mixture questions Parallel processing of all twelve 10 000 cycle Markov chains was completed by 11 pm Within hours Cybergenetics emailed the DA a preliminary match report on the suspect a 15 contributor to each three person mixture TrueAllele match statistics for the two evidence items were

    Original URL path: http://www.cybgen.com/information/presentations/2014/ISHI/Perlin-TrueAllele-speed-for-Grand-Jury-need-same-day-reporting-of-complex-mixtures/page.shtml (2016-02-12)
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  • Cybergenetics :: Assessing TrueAllele® genotype identification on DNA Mixtures containing up to five unknown contributors
    composition can help predict an expected LR outcome in a particular case This randomized experimental design examined 40 DNA mixture items The 4 mixture sets had 2 3 4 or 5 contributors with each item specified as a random mixture weighting of randomly assigned known references Both normal 1 ng and low 200 pg template amounts were studied for a total of 8 groups 4 contributor numbers x 2 template amounts each having 10 mixture items The mixture weight MW of each item s contributors had a predetermined design value but was subject to laboratory variation For each item the TrueAllele system computed two MW estimates one using all the known genotypes and the other with all genotypes unknown MW was also computed manually on the 2 contributor items There was a strong association r2 0 999 between the three computed MWs for an item and less r2 0 907 with the design value p Following a procedure used in a previous validation study 1 scatterplots were developed comparing a contributor s known DNA quantity logarithm of MW x total DNA x axis versus its identification information log of LR y axis This approach permitted examination of all the match results all contributors of all items within their groups across a single statistical analysis The scatterplots of positive match results were roughly linear r2 0 638 showing expected log LR reductions for equal MWs and high DNA amounts The average regression slope was 12 66 log LR log DNA p Analysis of covariance ANCOVA of the eight groups showed different x intercept values but no significant difference in slope p 0 348 0 05 This slope invariance was observed across four different contributor numbers 2 3 4 and 5 and DNA template amounts 200 pg and 1 ng This invariance

    Original URL path: http://www.cybgen.com/information/presentations/2014/AAFS/Perlin-Assessing-TrueAllele-Genotype-Identification-on-DNA-Mixtures-Containing-up-to-Five-Unknown-Contributors/page.shtml (2016-02-12)
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  • Cybergenetics :: Evaluating the specificity of genotypic inference with TrueAllele Casework software
    between known donor and non donor genotypes was achieved with as little as 62 5pg Average computer inferred genotype specificity between donor and non donor profiles was over 13 log units for two person mixtures 5 log units for three person mixtures and 4 log units for four person mixtures Results from this study show that probabilistic genotyping match statistics were both reproducible and specific to all known donor profiles The forensic literature has increasingly made recommendations for the use of probabilistic genotyping including most recently a strong encouragement from the DNA Commission of the International Society of Forensic Genetics ISFG to adopt likelihood ratio based approaches that include drop in and drop out for solving mixed template samples TrueAllele Casework Cybergenetics is a fully continuous Bayesian method that uses an iterative Markov chain Monte Carlo MCMC method to infer genotypes from evidentiary profiles and compute DNA match statistics and can easily accommodate drop in and drop out By preserving more identification information the computer is also able to add increased specificity to genotypic inference ultimately resulting in a high degree of separation between known donor and non donor likelihood ratios The high genotype specificity observed with this approach can then be translated into simplified DNA match reporting based on likelihood ratio calculations Uncertainty exists in virtually all fields of science In forensic STR analysis this uncertainty may take the form of partially recovered genotypes complex mixture profiles or an inability to accurately provide weight of evidence All currently used threshold based methods attempt to address uncertainty by either discarding or altering observed DNA data resulting in a loss of valuable genetic information with potential costs to public safety By modeling all observed peak height variation with MCMC computer based genotype inference can overcome stochastic effects and produce more scientifically

    Original URL path: http://www.cybgen.com/information/presentations/2014/AAFS/Caponera-Evaluating-the-specificity-of-genotypic-inference-with-TrueAllele-Casework-software/page.shtml (2016-02-12)
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  • Cybergenetics :: Getting past first Bayes with DNA mixtures
    years ago the Rev Thomas Bayes showed us how to update our belief in hypotheses probability by examining how well those hypotheses explain observed data likelihood Bayes has us use all the data and consider all hypotheses Bayesian genotype inference for each contributor at every genetic locus begins with a prior belief that the chance of observing an allele pair before seeing data is proportional to its population prevalence Careful examination of STR data then uses a likelihood function to concentrate probability on those genotype values that best explain the laboratory data This objectively inferred genotype associates a posterior probability with every allele pair multiplying prior and likelihood A DNA match statistic assesses the strength of match between evidence and reference genotypes relative to coincidence This Bayesian likelihood ratio LR weighs two competing hypotheses either the reference individual contributed DNA to the evidence or he did not based on the observed STR data Bayesian beginners often make mistakes They may fail to use all peak data or not consider all genotype hypotheses They can confuse likelihood chance of data given hypothesis with probability chance of hypothesis given data A beginner will apply complex formulas when a simple ratio would suffice

    Original URL path: http://www.cybgen.com/information/presentations/2013/ISHI/Perlin-Getting-Past-First-Bayes-with-DNA-Mixtures/page.shtml (2016-02-12)
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  • Cybergenetics :: Commonwealth of Pennsylvania v. Kevin James Foley
    an hour east of Pittsburgh PA Dr Yelenic who was living alone at the time had exsanguinated onto his living room floor On the coffee table splattered with his blood was the unsigned divorce document from his estranged wife Michelle She was living with her boyfriend Pennsylvania state trooper Kevin Foley John Yelenic s fingernails had DNA that tied trooper Foley to the crime with a match statistic of 13 000 Prior to Mr Foley s February 2008 preliminary hearing his defense lawyer Richard Galloway said that the DNA did not rule out other suspects because there was a one in 13 000 chance it came from someone else Moreover said his lawyer DNA often identifies suspects to the exclusion of billions or trillions of others Cybergenetics put the electronic DNA mixture data into its TrueAllele machine asking the computer to solve the problem and help identify the unknown contributor The computer worked on our questions over a weekend On Monday morning I reviewed the results and phoned prosecutor Anthony Krastek with the TrueAllele answer The DNA under Dr Yelenic s fingernails matched Kevin Foley with a statistic in the hundreds of billions Further calculations would later refine this number

    Original URL path: http://www.cybgen.com/information/presentations/2012/ISHI/Perlin-Commonwealth-of-Pennsylvania-v-Kevin-James-Foley/page.shtml (2016-02-12)
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